SQLite

1. The database is written by version 3.7.0 or greater, then
2. The database file is written to by a version earlier than 3.7.0 and the write operation causes the database file to shrink (either because data was removed from the db in auto-vacuum mode or because "PRAGMA incremental_vacuum" was executed in incr-vacuum mode).

This leaves the database in a state where 3.7.0 and greater report that it is corrupt (and no data can be read from it). It is not actually corrupt, and all data can still be read by earlier versions.

A database can be "repaired" by vacuuming it with a version earlier than 3.7.0.

   SQLite version 3.7.6
   Enter ".help" for instructions
   Enter SQL statements terminated with a ";"
   sqlite> PRAGMA auto_vacuum = 1;
   sqlite> CREATE TABLE t1(x);
   sqlite> .quit

   SQLite version 3.6.23.1
   Enter ".help" for instructions
   Enter SQL statements terminated with a ";"
   sqlite> DROP TABLE t1;
   sqlite> .quit

   SQLite version 3.7.6
   Enter ".help" for instructions
   Enter SQL statements terminated with a ";"
   sqlite> PRAGMA integrity_check;
   Error: database disk image is malformed

drh added on 2011-02-09 18:39:32:
The database can also be "repaired" in SQLite version 3.7.5 and later by using

PRAGMA writable_schema=ON;

Immediately after opening the connection, and then running VACUUM (or any other write operation) on the database.